The bithorax complex in the fruit fly, Drosophila melanogaster, is a cluster of genes that determine the identities of the segments in the posterior half of the fly. In animals that lack these genes, all the abdominal segments develop as copies of the middle thoracic segment. The cluster is large, over 300 kb, and it shows a striking organization. There is a regulatory region controlling the fate of each body segment, and these regions are aligned on the chromosome in the order of the segments they affect. The complex appears to have a different structure in each segment, with the unused regulatory domains kept globally repressed. The repression is maintained by a group of genes called the Polycomb family. In animals lacking Polycomb, all the regulatory regions become active, and all the segments develop like the eighth abdominal segment. Polycomb protein is bound to specific sites in the complex, Polycomb Response Elements, and there is apparently one such site per regulatory region. The bithorax complex contains only three protein coding transcription units that affect segmental identity. But there are also many non-coding RNAs, different ones in different segments. There are suggestions that some non-coding RNAs, appearing early in development, may determine the structure of the complex by affecting the Polycomb Response Elements. We plan to remove or truncate several of the non-coding RNAs, and look for changes in the Polycomb Response Elements, or other indications of non-coding RNA function. Cooperation among Polycomb Response Elements will be investigated, as well as their interaction with early acting enhancers. Tools will be developed to map proteins bound to the bithorax complex, one segment at a time.